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Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ILN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.928 α = 90 b = 87.135 β = 90 c = 156.193 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9793 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 43.57 100 0.995 1.6 7.1 19202
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.743 1.6 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ILN 2.1 43.57 19149 950 99.901 0.199 0.1972 0.2047 0.242 0.2493 31.623
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.867 4.613 -2.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.792 r_dihedral_angle_4_deg 17.231 r_dihedral_angle_3_deg 14.432 r_dihedral_angle_1_deg 8.763 r_lrange_it 6.307 r_lrange_other 6.281 r_scangle_it 4.888 r_scangle_other 4.815 r_mcangle_it 3.979 r_mcangle_other 3.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.792 r_dihedral_angle_4_deg 17.231 r_dihedral_angle_3_deg 14.432 r_dihedral_angle_1_deg 8.763 r_lrange_it 6.307 r_lrange_other 6.281 r_scangle_it 4.888 r_scangle_other 4.815 r_mcangle_it 3.979 r_mcangle_other 3.978 r_scbond_it 3.51 r_scbond_other 3.47 r_mcbond_it 2.758 r_mcbond_other 2.757 r_angle_refined_deg 1.738 r_angle_other_deg 1.312 r_symmetry_xyhbond_nbd_refined 0.305 r_nbd_other 0.263 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.201 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.168 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2035 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction PHASER phasing BUCCANEER model building Coot model building